My document is very long and include a lot of references.
When I click on the button of “Update citations and Bibliography” in my Word,
it is asked always for the parenthetical statements which are not citations. I.e… (see eq. 12)
Do I have to state always those statements are not citations ? Or is there another way to disregard or eliminate this?
Secondly, Endnote sometimes adding citations instead of statements in brackets, unexpectedly. I always check the full document whether Endnote inserts a wrong citation or not.
I suspect that you have inadvertently changed the “temporary citation” marks to plain parentheses rather than curly or square parentheses. There are two places you can change this setting. The global one in Edit>preferences in Endnote program under "Temporary Citations and the delimiters should be curly brackets (unless you use them often for other things, like equations, and then you might want to use ~ and & or square brackets any unique pair that you don’t use for anything else).
I think setting that there will automatically change any new or existing document, but after changing that, you can look at the Format Bibliography dialog box and in my test in ENX6, it was already altered). Then try running the "Update Citations & Bibliography) and you should stop getting that query.
It shouldn’t try to interpret a comment as a citation, if it isn’t in the chosen temporary citation delimiters, so I am not sure what you are seeing? Can you give an example?